Variant report

Variant	rs3924843
Chromosome Location	chr2:20381830-20381831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20339841..20342282-chr2:20379713..20382419,2	MCF-7	breast:
2	chr2:20380951..20386083-chr2:20391129..20397009,8	MCF-7	breast:
3	chr2:20301825..20304525-chr2:20380174..20381913,2	MCF-7	breast:
4	chr2:20323258..20325480-chr2:20380039..20381857,2	MCF-7	breast:
5	chr2:20374283..20377217-chr2:20380767..20383134,3	MCF-7	breast:
6	chr2:20309325..20314922-chr2:20379425..20384303,7	MCF-7	breast:
7	chr2:20251074..20253926-chr2:20378631..20381986,3	MCF-7	breast:
8	chr2:20366533..20369508-chr2:20380029..20382114,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000223734	Chromatin interaction
ENSG00000068697	Chromatin interaction
ENSG00000200763	Chromatin interaction
ENSG00000266059	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11096642	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11096643	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11673796	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11694854	0.89[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12475147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35755926	0.82[ASN][1000 genomes]
rs4297841	0.88[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs4358082	0.89[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4462755	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55857480	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55874308	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56388073	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6419087	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6531217	0.82[ASN][1000 genomes]
rs6531218	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7559900	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1004947	chr2:20342264-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv997958	chr2:20349343-20386339	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1005524	chr2:20349343-20388138	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv998067	chr2:20350751-20386339	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1001531	chr2:20350751-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1007926	chr2:20350751-20393557	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	esv991709	chr2:20376888-20383371	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3924843	MFSD2B	cis	parietal	SCAN
rs3924843	MATN3	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20367800-20383600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:20373000-20384200	Weak transcription	Fetal Lung	lung
3	chr2:20376200-20386200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:20377200-20386200	Enhancers	Esophagus	oesophagus
5	chr2:20377200-20388200	Enhancers	Stomach Mucosa	stomach
6	chr2:20377400-20382200	Enhancers	Colonic Mucosa	Colon
7	chr2:20377400-20384800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:20377400-20390000	Enhancers	Placenta	Placenta
9	chr2:20377600-20386000	Enhancers	Liver	Liver
10	chr2:20378400-20386600	Enhancers	HMEC	breast
11	chr2:20379400-20384400	Weak transcription	Fetal Kidney	kidney
12	chr2:20380000-20385200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:20380200-20382400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:20380200-20383600	Weak transcription	Pancreas	Pancrea
15	chr2:20380200-20384600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:20380400-20383400	Weak transcription	Fetal Intestine Large	intestine
17	chr2:20380400-20383600	Weak transcription	Fetal Intestine Small	intestine
18	chr2:20380400-20383600	Enhancers	HepG2	liver
19	chr2:20380400-20384600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:20380400-20385000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:20380400-20385800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr2:20380800-20382000	Enhancers	Lung	lung
23	chr2:20381000-20382000	Enhancers	A549	lung
24	chr2:20381000-20384200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:20381400-20386400	Enhancers	NHEK	skin
26	chr2:20381400-20387200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:20381600-20382000	Enhancers	K562	blood
28	chr2:20381600-20386200	Enhancers	Hela-S3	cervix
29	chr2:20381600-20387400	Enhancers	NH-A	brain
30	chr2:20381600-20388000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:20381800-20382000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:20381800-20382200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:20381800-20382600	Weak transcription	Gastric	stomach
34	chr2:20381800-20384600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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